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Volumn 88, Issue 3, 2013, Pages 325-337

In silico mining of novel microRNAs from coffee (Coffea arabica) using expressed sequence tags

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; COFFEA ARABICA;

EID: 84881033460     PISSN: 14620316     EISSN: None     Source Type: Journal    
DOI: 10.1080/14620316.2013.11512973     Document Type: Article
Times cited : (13)

References (53)
  • 1
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • AMBROS, V. (2004). The functions of animal microRNAs. Nature, 431, 350-355.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 3
    • 0242361521 scopus 로고    scopus 로고
    • Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes
    • AUKEMAN, M. J. and SAKAI, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell, 15, 2730-2741.
    • (2003) Plant Cell , vol.15 , pp. 2730-2741
    • Aukeman, M.J.1    Sakai, H.2
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics biogenesis mechanism and function
    • BARTEL, D. P. (2004). MicroRNAs: genomics biogenesis mechanism and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • BARTEL, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 6
    • 3843089328 scopus 로고    scopus 로고
    • Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
    • BONNET, E., WUYTS, J., ROUZE, P. and VAN DE PEER, Y. (2004). Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proceedings of the National Academy of Sciences of the USA, 101, 11511-11516.
    • (2004) Proceedings of the National Academy of Sciences of the USA , vol.101 , pp. 11511-11516
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    van de Peer, Y.4
  • 7
    • 1642366133 scopus 로고    scopus 로고
    • A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    • CHEN, X. (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303, 2022-2025.
    • (2004) Science , vol.303 , pp. 2022-2025
    • Chen, X.1
  • 9
    • 33748346026 scopus 로고    scopus 로고
    • Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
    • DIDIANO, D. and HOBERT, O. (2006). Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nature Structural and Molecular Biology, 13, 849-851.
    • (2006) Nature Structural and Molecular Biology , vol.13 , pp. 849-851
    • Didiano, D.1    Hobert, O.2
  • 11
    • 27844526222 scopus 로고    scopus 로고
    • A miRNA involved in phosphate-starvation response in Arabidopsis
    • FUJII, H., CHIOU, T. J., LIN, S. I., AUNG, K. and ZHU, J. K. (2005). A miRNA involved in phosphate-starvation response in Arabidopsis. Current Biology, 15, 2038-2043.
    • (2005) Current Biology , vol.15 , pp. 2038-2043
    • Fujii, H.1    Chiou, T.J.2    Lin, S.I.3    Aung, K.4    Zhu, J.K.5
  • 12
    • 0042421751 scopus 로고    scopus 로고
    • The Arabidopsis Basic/Helix-Loop-Helix transcription factor family
    • GABRIELA, T. O., ENAMUL, H. and PETER, H. Q. (2003). The Arabidopsis Basic/Helix-Loop-Helix transcription factor family. The Plant Cell, 15, 1749-1770.
    • (2003) The Plant Cell , vol.15 , pp. 1749-1770
    • Gabriela, T.O.1    Enamul, H.2    Peter, H.Q.3
  • 18
    • 79954569860 scopus 로고    scopus 로고
    • High AU content: A signature of up-regulated miRNA in cardiac diseases
    • GUPTA, R., SONI, N., PATNAIK, P., SOOD, I., SINGH, R., RAWAL, K. and RANI, V. (2010). High AU content: a signature of up-regulated miRNA in cardiac diseases. Bioinformation, 5(3), 132-135.
    • (2010) Bioinformation , vol.5 , Issue.3 , pp. 132-135
    • Gupta, R.1    Soni, N.2    Patnaik, P.3    Sood, I.4    Singh, R.5    Rawal, K.6    Rani, V.7
  • 19
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment 291 editor and analysis 292 program for Windows 95/98/NT
    • HALL, T.A. (1999) BioEdit: a user-friendly biological sequence alignment 291 editor and analysis 292 program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
    • (1999) Nucleic Acids Symposium Series , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 20
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple-turnover RNAi enzyme complex
    • HUTVAGNER, G. and ZAMORE, P.D. (2002). A microRNA in a multiple-turnover RNAi enzyme complex. Science, 297, 2056-2060.
    • (2002) Science , vol.297 , pp. 2056-2060
    • Hutvagner, G.1    Zamore, P.D.2
  • 21
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant microRNAs and their targets including a stress-induced miRNA
    • JONES-RHOADES, M. W. and BARTEL, D. P. (2004). Computational identification of plant microRNAs and their targets including a stress-induced miRNA. Molecular Cell Biology, 6, 787-799.
    • (2004) Molecular Cell Biology , vol.6 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 22
    • 0037320231 scopus 로고    scopus 로고
    • P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function
    • KASSCHAU, K. D., XIE, Z., ALLEN, E., LLAVE, C., CHAPMAN, E. J., KRIZAN, K. A. and CARRINGTON, J. C. (2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Developmental Cell, 4, 205-217
    • (2003) Developmental Cell , vol.4 , pp. 205-217
    • Kasschau, K.D.1    Xie, Z.2    Allen, E.3    Llave, C.4    Chapman, E.J.5    Krizan, K.A.6    Carrington, J.C.7
  • 23
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 11-120.
    • (1980) Journal of Molecular Evolution , vol.16 , pp. 11-120
    • Kimura, M.1
  • 24
    • 0035955374 scopus 로고    scopus 로고
    • Identification of novel genes coding for small expressed RNAs
    • LAGOS-QUINTANA, M., RAUHUT, R., LENDECKEL, W. and TUSCHL, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294, 853-8.
    • (2001) Science , vol.294 , pp. 853-858
    • Lagos-Quintana, M.1    Rauhut, R.2    Lendeckel, W.3    Tuschl, T.4
  • 26
    • 0035955366 scopus 로고    scopus 로고
    • An extensive class of RNAs in Caenorhabditis elegans
    • LEE, R. C. and AMBROS, V. (2001). An extensive class of RNAs in Caenorhabditis elegans. Science, 294, 862-864.
    • (2001) Science , vol.294 , pp. 862-864
    • Lee, R.C.1    Ambros, V.2
  • 27
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • LEE, R. C., FEINBAUM, R. L. and AMBROS, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 28
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • LEWIS, B.P., BURGE, C.B. and BARTEL, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 29
    • 3242733283 scopus 로고    scopus 로고
    • MicroRNAs: More than a role in plant development?
    • LLAVE, C. (2004). MicroRNAs: more than a role in plant development? Molecular Plant Pathology, 5, 361-366.
    • (2004) Molecular Plant Pathology , vol.5 , pp. 361-366
    • Llave, C.1
  • 30
    • 0035984059 scopus 로고    scopus 로고
    • Endogenous and silencing-associated small RNAs in plants
    • LLAVE, C., KASSCHAU, K., RECTOR, M. and CARRINGTON, J. (2002). Endogenous and silencing-associated small RNAs in plants. The Plant Cell, 14, 1605-1619.
    • (2002) The Plant Cell , vol.14 , pp. 1605-1619
    • Llave, C.1    Kasschau, K.2    Rector, M.3    Carrington, J.4
  • 32
    • 2942697259 scopus 로고    scopus 로고
    • MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative and floral organs
    • MALLORY, A.C., DUGAS, D.V., BARTEL, D. P. and BARTEL, B. (2004a). MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative and floral organs. Current Biology, 14, 1035-1046.
    • (2004) Current Biology , vol.14 , pp. 1035-1046
    • Mallory, A.C.1    Dugas, D.V.2    Bartel, D.P.3    Bartel, B.4
  • 34
    • 0036738077 scopus 로고    scopus 로고
    • Short RNAs can identify new candidate transposable element families in Arabidopsis
    • METTE, M. F., VAN DERWINDEN, J., MATZKE, M. and MATZKE, A. J. (2002). Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiology, 130, 6-9.
    • (2002) Plant Physiology , vol.130 , pp. 6-9
    • Mette, M.F.1    van Derwinden, J.2    Matzke, M.3    Matzke, A.J.4
  • 36
    • 0037015239 scopus 로고    scopus 로고
    • Carpel factory, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana
    • PARK, W., LI, J., SONG, R., MESSING, J. and CHEN, X. (2002). Carpel factory, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology, 12, 1484-1495.
    • (2002) Current Biology , vol.12 , pp. 1484-1495
    • Park, W.1    Li, J.2    Song, R.3    Messing, J.4    Chen, X.5
  • 37
    • 34247624029 scopus 로고    scopus 로고
    • Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags
    • QIU, C. X., XIE, F. L., ZHU, Y.Y., GUO, K., HUANG, S.Q., NIE, L. and YANG Z.M. (2007). Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene, 395, 49-61.
    • (2007) Gene , vol.395 , pp. 49-61
    • Qiu, C.X.1    Xie, F.L.2    Zhu, Y.Y.3    Guo, K.4    Huang, S.Q.5    Nie, L.6    Yang, Z.M.7
  • 40
    • 0023375195 scopus 로고
    • The neighbour-joining method: A new method for reconstructing phylogenetic trees
    • SAITOU, N. and NEI, N. (1987). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, N.2
  • 41
    • 54549088851 scopus 로고    scopus 로고
    • In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum)
    • SINGH, J. and NAGARAJU, J. (2008). In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum). Insect Molecular Biology, 17, 427-436.
    • (2008) Insect Molecular Biology , vol.17 , pp. 427-436
    • Singh, J.1    Nagaraju, J.2
  • 42
    • 4043074968 scopus 로고    scopus 로고
    • Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    • SUNKAR, R. and ZHU, J. K. (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16, 2001-2019.
    • (2004) Plant Cell , vol.16 , pp. 2001-2019
    • Sunkar, R.1    Zhu, J.K.2
  • 43
    • 33747505089 scopus 로고    scopus 로고
    • Post-transcriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by down-regulation of miR398 and important for oxidative stress tolerance
    • SUNKAR, R., KAPOOR, A. and ZHU, J. K. (2006). Post-transcriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by down-regulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18, 2051-2065.
    • (2006) Plant Cell , vol.18 , pp. 2051-2065
    • Sunkar, R.1    Kapoor, A.2    Zhu, J.K.3
  • 44
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • TAMURA, K., PETERSON, D., PETERSON, N., STECHER, G., NEI, M. and KUMAR, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 45
    • 0942301280 scopus 로고    scopus 로고
    • The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'-UTR
    • VELLA, M.C., CHOI, E.Y., LIN, S. Y, REINERT, K. and SLACK, F.J. (2004) The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'-UTR. Genes and Development, 18, 132-137.
    • (2004) Genes and Development , vol.18 , pp. 132-137
    • Vella, M.C.1    Choi, E.Y.2    Lin, S.Y.3    Reinert, K.4    Slack, F.J.5
  • 46
    • 33947411951 scopus 로고    scopus 로고
    • Computational identification of novel microRNAs and targets in Brassica napus
    • XIE, F. L., HUANG, S. Q., GUO, K., XIANG, A. L., ZHU, Y. Y., NIE, L. and YANG, Z. M. (2007). Computational identification of novel microRNAs and targets in Brassica napus. FEBS Letters, 581, 1464-1474.
    • (2007) FEBS Letters , vol.581 , pp. 1464-1474
    • Xie, F.L.1    Huang, S.Q.2    Guo, K.3    Xiang, A.L.4    Zhu, Y.Y.5    Nie, L.6    Yang, Z.M.7
  • 47
    • 41949100147 scopus 로고    scopus 로고
    • Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum)
    • YIN, Z., LI, C., HAN, X. and SHEN, F. (2008). Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414, 60-66.
    • (2008) Gene , vol.414 , pp. 60-66
    • Yin, Z.1    Li, C.2    Han, X.3    Shen, F.4
  • 48
    • 27844495281 scopus 로고    scopus 로고
    • Identification and characterization of new plant microRNAs using EST analysis
    • ZHANG, B. H., PAN, X. P., WANG, Q. L., COBB, G. P. and ANDERSON, T. A. (2005). Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15, 336-360.
    • (2005) Cell Research , vol.15 , pp. 336-360
    • Zhang, B.H.1    Pan, X.P.2    Wang, Q.L.3    Cobb, G.P.4    Anderson, T.A.5
  • 49
    • 33745156778 scopus 로고    scopus 로고
    • Identification of 188 conserved maize microRNAs and their targets
    • ZHANG, B. H., PAN, X. and ANDERSON, T. A. (2006a). Identification of 188 conserved maize microRNAs and their targets. FEBS Letters, 580, 3753-3762.
    • (2006) FEBS Letters , vol.580 , pp. 3753-3762
    • Zhang, B.H.1    Pan, X.2    Anderson, T.A.3
  • 52
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • ZUKER, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 53
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • ZUKER, M. and STIEGLER, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research, 9, 133-148.
    • (1981) Nucleic Acids Research , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


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